Merge devel to master for release 2.53.0

.github/workflows/run-tests.yml

@@ -12,7 +12,7 @@ jobs:
         shell: bash -l -e -o pipefail {0}
 
     env:
-      SINGULARITY_VERSION: "3.11.1"
+      SINGULARITY_VERSION: "4.2.2"
       PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
       NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
       WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
@@ -87,6 +87,7 @@ jobs:
           sudo apt-get install -qq libgd-dev libgd-text-perl # For npg_tracking
           sudo apt-get install -qq liblzma-dev # For npg_qc
           sudo apt-get install -qq pigz        # for BioNano run publication in npg_irods
+          sudo apt-get install -qq libdevel-patchperl-perl # For perlbrew
 
       - name: "Install Singularity"
         run: |

Changes

@@ -1,5 +1,17 @@
 Unreleased
 
+Release 2.53.0 (2025-01-17)
+ - Fixed perlbrew installation by installing libdevel-patchperl-perl in
+   GitHub runner.
+ - Allow for naming differences in unbarcoded bam files from SMRT Link
+   deplexing
+ - Pacbio - in v13.1 onboard processing changes
+ - Update the annotators of Illumina and Pacbio to accept sample_uuid and
+   sample_lims
+ - Remove unused ONT files and references
+ - Install libdevel-patchperl-perl in GitHub runner
+ - Bump Singularity to 4.2.2 for CI
+
 Release 2.52.0 (2024-12-02)
  - Minor changes and tests for IsoSeq csi publishing
  - collect pipeline central, postqc and product release logs from BAM_basecalls

lib/WTSI/NPG/HTS/Illumina/Annotator.pm

@@ -418,10 +418,12 @@ sub make_sample_metadata {
   my $method_attr =
     {sample_accession_numbers => $SAMPLE_ACCESSION_NUMBER,
      sample_ids               => $SAMPLE_ID,
+     sample_lims              => $SAMPLE_LIMS,
      sample_names             => $SAMPLE_NAME,
      sample_public_names      => $SAMPLE_PUBLIC_NAME,
      sample_common_names      => $SAMPLE_COMMON_NAME,
      sample_supplier_names    => $SAMPLE_SUPPLIER_NAME,
+     sample_uuids             => $SAMPLE_UUID,
      sample_cohorts           => $SAMPLE_COHORT,
      sample_donor_ids         => $SAMPLE_DONOR_ID};
 
@@ -585,7 +587,7 @@ Keith James <kdj@sanger.ac.uk>, Iain Bancarz <ib5@sanger.ac.uk>
 
 =head1 COPYRIGHT AND DISCLAIMER
 
-Copyright (C) 2015, 2016, 2017, 2018, 2019 Genome Research Limited.
+Copyright (C) 2015, 2016, 2017, 2018, 2019, 2024 Genome Research Limited.
 All Rights Reserved.
 
 This program is free software: you can redistribute it and/or modify

lib/WTSI/NPG/HTS/Metadata.pm

@@ -9,8 +9,6 @@ use Exporter qw[import];
 
 ## no critic (Modules::ProhibitAutomaticExportation)
 our @EXPORT = qw[
-                 $EXPERIMENT_NAME
-                 $GRIDION_DEVICE_ID
                  $LIBRARY_TYPE
                  $SEQCHKSUM
                  $HUMAN
@@ -24,9 +22,6 @@ our $VERSION = '';
 
 # Annotation
 
-our $EXPERIMENT_NAME   = 'experiment_name';
-our $GRIDION_DEVICE_ID = 'device_id';
-
 our $LIBRARY_TYPE = 'library_type';
 our $SEQCHKSUM    = 'seqchksum';
 

lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm

@@ -4,6 +4,7 @@ use namespace::autoclean;
 use English qw[-no_match_vars];
 use File::Basename;
 use File::Spec::Functions qw[catdir];
+use List::AllUtils qw[any];
 use JSON;
 use Moose;
 use MooseX::StrictConstructor;
@@ -399,8 +400,7 @@ sub _get_tag_name_from_fname {
 
 sub _is_allowed_fname {
   my ($self, $file, $fnames) = @_;
-  my @exists = grep { $file =~ m{[.] $_ [.]}smx } @{ $fnames };
-  return @exists == 1 ? 1 : 0;
+  return (any {  $file =~ m{[.] $_ [.]}smx  } @{ $fnames } );
 }
 
 sub _dest_path {

lib/WTSI/NPG/HTS/PacBio/Annotator.pm

@@ -161,6 +161,8 @@ sub make_sample_metadata {
   my @samples = map { $_->sample } @run_records;
   my $method_attr = {accession_number => $SAMPLE_ACCESSION_NUMBER,
                      id_sample_lims   => $SAMPLE_ID,
+                     id_lims          => $SAMPLE_LIMS,
+                     uuid_sample_lims => $SAMPLE_UUID,
                      name             => $SAMPLE_NAME,
                      public_name      => $SAMPLE_PUBLIC_NAME,
                      common_name      => $SAMPLE_COMMON_NAME,
@@ -319,7 +321,7 @@ Keith James <kdj@sanger.ac.uk>
 
 =head1 COPYRIGHT AND DISCLAIMER
 
-Copyright (C) 2016, 2017 Genome Research Limited. All Rights Reserved.
+Copyright (C) 2016, 2017, 2024 Genome Research Limited. All Rights Reserved.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the Perl Artistic License or the GNU General

lib/WTSI/NPG/HTS/PacBio/RunPublisher.pm

@@ -643,7 +643,7 @@ sub publish_image_archive {
       elsif ($process_type eq $ONINST_REVIO1) {
         $file_types  = q{ccs_report.txt|fail_reads.lima_counts.txt|}.
           q{fail_reads.lima_summary.txt|hifi_reads.lima_counts.txt|}.
-          q{hifi_reads.lima_summary.txt|summary.json|fail_reads.json|hifi_reads.json|}.
+          q{hifi_reads.lima_summary.txt|summary.json|hifi_reads.json|}.
           q{ccs_report.json|fail_reads.unassigned.json|hifi_reads.unassigned.json};
       }
       elsif ($process_type eq $ONINST_REVIO2) {

t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm

@@ -221,8 +221,10 @@ sub update_secondary_metadata_tag1_no_spike_human : Test(12) {
        {attribute => $SAMPLE_COMMON_NAME,       value => 'Mus musculus'},
        {attribute => $SAMPLE_DONOR_ID,          value => '2905STDY6178180'},
        {attribute => $SAMPLE_ID,                value => '2376982'},
+       {attribute => $SAMPLE_LIMS,              value => 'SQSCP'},
        {attribute => $SAMPLE_PUBLIC_NAME,       value => 'UTX_IP_UTX_GTX_A'},
        {attribute => $SAMPLE_SUPPLIER_NAME,     value => 'UTX_IP_UTX_GTX_A'},
+       {attribute => $SAMPLE_UUID,              value => '4e0f6640-40f7-11e5-998e-3c4a9275d6c6'},
        {attribute => $STUDY_NAME,
         value     => 'Analysis of the chromatin state of mouse stem and progenitor cell compartment'},
        {attribute => $STUDY_ACCESSION_NUMBER,   value => 'ERP004563'},